Scientific analyses of the traditional materials and methods in thangka production are uncommon, as thangkas are sacred objects, the sampling of which is discouraged, in order to preserve their integrity. This study builds on this important ethical challenge and presents a three-stage methodology that systematically delves deeper into each layer of the composition, successfully enabling the investigation of different phases of production. In the first stage, visual examination of the painting, including observations under magnification, was used to assess its condition. In the next step, the infrared reflected (IRR) and short-wave infrared (SWIR) images revealed the underdrawing and instances of modifications as well as colour notations. Additionally, ultraviolet-induced visible luminescence (UVL), infrared-reflected false colour (IRRFC) and X-ray images provided important preliminary information on the colourants present, the nature of the underdrawing, and the painting technique. In the final stages, fibre optic reflectance (FORS), Fourier-transform infrared (FTIR) and Raman spectroscopies confirmed the identity of many of the pigments (cinnabar/vermillion, minium, iron oxide, malachite, azurite, indigo, Indian lac), the ground and the binder used for the blue and green paint layers. In addition, key details of practices and materials were revealed, that may indicate provenance or other information of scholarly importance. These will constitute a helpful comparison to existing and future studies of other thangkas.